EMBOSS: Project Meeting (Fri 27th June 2003)


HGMP: Gary Williams, Alan Bleasby, Tim Carver, Jon Ison, Claude Beazley
Lion: Thomas Laurent
Cambridge Uni:
EBI: Peter Rice

Apologies: Dave Judge

Minutes of the last meeting

Minutes of the meeting of 30th May 2003 are here

1. Action points

From this meetings:
Fix domainatrix test data on failed cases; Peter will provide cases. (JCI, 2003-06-27)
Run acdvalid on all applications. (PMR, 2003-06-27)

From previous meetings:
ACD docs need updating (action PMR, 2003-02-21)
MEME documentation is required (action AJB, 2003-02-21)
Look into binary downloads for MAC OS 10 (AL, 2003-03-07)
Research automatic conversion of html to docbook (Adam can provide a script to help with the reformatting) (TJS, 2003-03-07)
Provide documentation for propehcy (AJB, 2003-03-21) 1.2 Progress on action points
Approach Malcolm Herbert about RedHat Linux distribution for bioinformatics. (DC, 2003-03-21)
Provide GW with text thanking providers of emboss machines for their support (AJB, 2003-03-21)
Test domainatrix test data (JCI, 2003-05-16)
Prepare extra talks for EMBOSS Programming Course (JCI, 2003-05-16)

The following action points are postponed until further notice
Prepare training course / demo on "Documentation of EMBOSS Software" (the use of XML Mind etc) (DC & TJS, 2003-03-07)
Preliminary look into industry funding for EMBOSS (JCI, 2003-03-21)

2. Software Development

2.1 -graph data update for spin (PMR)
Peter has committed changes so that -graph data now works; it reports to standard output the graphs that have been written. He will work on -graph xml next.

2.2 PCRE library (PMR)

PCRE is a regular expression library in EMBOSS. Peter reported that he is changing the existing ajReg to ajSreg, the new ajReg will use PCRE, and then the Henry Spencer library in EMBOSS will be discontinued.

2.3 Phylip 3.6 (PMR)

Peter reported that Phylip is next on his list after PCRE. Alan has provided the original version of the source of the the version of Phylip that is currently in EMBOSS. Phylip 3.6 is an alpha release although users have reported it is very stable. Peter suggested keeping both running for the time being. An EMBASSY package called 'phylip_new' will be created for the new version. Peter reported that he added ajFileNewOutC.
Alan reported that he wrote and committed a generalised degap function which takes a char * of characters to remove from a string.

4. Documentation & Training

Alan reported that we've received confirmation of funding for the EMBOSS development project.

5. Administration

7. AOB

8. Date Of Next Meeting

Next meeting to be held at 9.30 on July 11 2003, Loft Room 2